X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=114750e71e4c5cb127cf4b9407bd1841bb8aa622;hb=8ef6687c1f586285d01c000cc5e359bf9c07c717;hp=9e2a08b2a493fec7ed717505d7d02112a8530b49;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 9e2a08b..114750e 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,7 +13,7 @@
 
 //***************************************************************************************************************
 
-ReverseSeqsCommand::ReverseSeqsCommand(string option){
+ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
 	try {
 		abort = false;
 		
@@ -22,52 +22,65 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"fasta"};
+			string Array[] =  {"fasta", "outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
 			
 			ValidParameters validParameter;
-		
+			map<string,string>::iterator it;
+			
 			//check to make sure all parameters are valid for command
-			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("fasta");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["fasta"] = inputDir + it->second;		}
+				}
+			}
+
 			//check for required parameters
 			fasta = validParameter.validFile(parameters, "fasta", true);
 			if (fasta == "not open") { abort = true; }
-			else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true;  }	
+			else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }	
 			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
+				outputDir = "";	
+				outputDir += hasPath(fasta); //if user entered a file with a path then preserve it	
+			}
+
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 //**********************************************************************************************************************
 
 void ReverseSeqsCommand::help(){
 	try {
-		cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
-		cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
-		cout << "The reverse.seqs command should be in the following format: " << "\n";
-		cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";	
+		m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+		m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+		m->mothurOut("The reverse.seqs command should be in the following format: \n");
+		m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");	
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ReverseSeqsCommand", "help");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 //***************************************************************************************************************
@@ -86,26 +99,34 @@ int ReverseSeqsCommand::execute(){
 		openInputFile(fasta, inFASTA);
 		
 		ofstream outFASTA;
-		string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
+		string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
 		openOutputFile(reverseFile, outFASTA);
 		
 		while(!inFASTA.eof()){
-			Sequence currSeq(inFASTA);
-			currSeq.reverseComplement();
-			currSeq.printSequence(outFASTA);
+			if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(reverseFile.c_str()); return 0; }
+			 
+			Sequence currSeq(inFASTA);  gobble(inFASTA);
+			if (currSeq.getName() != "") {
+				currSeq.reverseComplement();
+				currSeq.printSequence(outFASTA);
+			}
 		}
 		inFASTA.close();
 		outFASTA.close();
 		
+		if (m->control_pressed) {  remove(reverseFile.c_str()); return 0; }
+		
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut(reverseFile); m->mothurOutEndLine();	
+		m->mothurOutEndLine();
+
+		
 		return 0;
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ReverseSeqsCommand", "execute");
 		exit(1);
 	}
 }